Friday, March 29, 2013

In 1975, the skull of an ancient canid (a member of
the dog family) was discovered in Razboinichya cave within the Altai
Republic, a mountainous region in southern Siberia. The skull was
suspected to be that of a dog rather than a wolf or other canid. However, radiocarbon
dating showed the skull to be about 33,000 years old, which is more than double
the age of the oldest confirmed dog specimens. If the Altai skull was in fact a
dog, that would significantly set back the date of dog domestication. The problem
is that it's difficult to discriminate between early dog and wolf skulls. Researchers led by Anna
Druzhkova of the Siberian Branch of the Russian Academy of Sciences solved that
problem by doing mitochondrial DNA (mtDNA) analysis on the
skull. They showed that it is indeed from a dog. This means that dogs have been
around for a very long time, long before the invention of agriculture or the
wheel.

There is little doubt that dogs
are the domesticated descendents of grey wolves. There is, however, a fair bit
of controversy as to when those domestication events first occurred. We have
archeological evidence of the existence of dogs (as a distinct species from
wolves) at least 14,000 years ago, but they undoubtedly emerged much earlier.
Without DNA analysis, it’s difficult to prove whether ancient specimens are really
dogs rather than wolves. MtDNA, which is inherited only from the mother and
hence has a less complicated provenance, has been particularly helpful in
creating phylogenetic trees.

The scientists extracted mtDNA from the Altai skull and compared it to
the mtDNA of 72 different dogs, 30 wolves, 4 coyotes and 35
prehistoric canids. Most importantly, three of the wolf specimens were from fragments of
contemporaneous remains found within the same cave as the dog skull. If the Altai skull had belonged to a wolf, it should have most closely matched the other wolves living in the same area at the same time. This was not what the researchers found. Instead, the Altai
skull mtDNA most closely matched the DNA of dogs and was not closely related to
the wolves that coexisted with it.

We
still can’t say for sure when dogs first split off genetically from wolves.
However, these data suggest that it happened more than 33,000 years ago, by which point they were already separate species.

For some fascinating interviews about the origin of dog
domestication, listen to this episode of Skeptically Speaking.

Thursday, March 28, 2013

Who hasn’t occasionally felt like indulging in an online rant against an
injustice or an example of stupidity? The good news is that there are
myriad sites dedicated to just this activity. Whatever triggers your ire,
there’s a website where you can pour out your vitriol to like-minded enraged
compatriots. The bad news is that you may not be doing yourself a favor if you
partake in this kind of venting.

Ryan Martin and his colleagues from the University of
Wisconsin-Green Bay gave 91 college students a Differential Emotions Scale
(DES) test to evaluate their levels of happiness, sadness, anger and/or fear on
a scale of 0 to 100. Immediately after assessing their current emotions, they
were asked to spend five minutes reading through the posts on a rant-site
(screen shots were used so that all participants read the exact same rants).
After reading the site, the subjects completed another DES. Next, the
volunteers were asked to spend five minutes writing their own anonymous rant on
any topic they chose. Upon completion, they filled out a final DES.

Reading the rants caused the average person’s happiness
levels to decrease and sadness levels to increase. However, the difference
wasn’t extreme. For both emotions, the post-reading levels were less than five
points different. Remember, this was on a scale of 100 possible points. Writing
their own rants affected participants more significantly. People’s happiness
decreased by ten points and their anger increased by close to fourteen points
after writing their screeds.

The subjects were each asked whether they’d like their own
rant posted onto the site they had been reading (though none were actually
posted regardless of preference). Those who wished to publish had experienced
more anger while reading posts than those who did not want their own vents
published. On the other hand, the people who were ready to publish their own
rants had less decrease in happiness while writing those rants than people who
didn’t want to publish. Interestingly, the subset of participants (7%) who said
they would go back to the rant site on their own time actually experienced an
increase in happiness while reading the site.

This
data suggests that for most people, reading and writing rants is
counterproductive. They were more angry and sad and less happy after engaging
in these activities. However, for the people who looked forward to publishing
their own rants, reading and writing rants seemed to be somewhat enjoyable. I
should point out that this was a small, highly subjective study with no
controls, and that the body of evidence about the value of catharsis is mixed. I
think the bottom line is that if you find that reading diatribes makes you
angry or anxious, it’s probably not the best activity for you. Personally, I’m
very selective about reading the comments on YouTube channels or blogs (except
mine, I love the comments on The Stochastic Scientist!). Martin, R., Coyier, K., VanSistine, L., & Schroeder, K. (2013). Anger on the Internet: The Perceived Value of Rant-Sites Cyberpsychology, Behavior, and Social Networking, 16 (2), 119-122 DOI: 10.1089/cyber.2012.0130.

Wednesday, March 27, 2013

Scientific American sponsors the ‘Iron Egghead Video Contest’. The goal of this contest is to explain an aspect of human anatomy or a biological function
using only the following props: paper (or other
writing surface), writing implement, rubberbands, paper clips, string, cups,
balls and yourself/yourselves in a two minute video.

Below, the grand prize winners explain
our adrenal glands in a way you won't forget.

Tuesday, March 26, 2013

We’ve all experienced the Doppler effect. This is what
causes the change in sound we hear as a siren approaches and then passes us.
The sound waves shift in frequency as each crest takes first shorter and
shorter and then longer and longer to reach us. According to researchers led by
Eugene Caruso of the University of Chicago, there is also a ‘temporal Doppler
effect’ that makes events in the future seem closer to us than events in the
past.

In one set of experiments, the scientists asked volunteers
to think ahead a specific amount of time in the future (a week, a month or a
year) and to think back the same amount of time in the past. The subjects
reported that the future seemed closer than the past. You can try this yourself
and see if you agree. We’re about equidistant from Christmas and the end of the
school year right now. Which seems closer?

One possible reason for this observation is that we perceive
time as moving, just like objects or sounds waves. We feel as if the past is
actually receding and the future approaching. If so, our own physical movements
might affect that perception. To test this, the researchers submersed
undergraduates in a virtual reality environment in which they moved either
forward or backward and then asked the students about their time perceptions.
Participants felt that the future was closer than the past when they were
moving forward but not when moving backward.

This is yet another example of how our brains fool us about
the world around us. And of course, I can’t end a story about time without my
favorite quotation, usually (but probably wrongly) attributed to Groucho Marx:

Monday, March 25, 2013

If you want people to do something, is it better to tell
them what wonderful things will happen if they do as you ask, or what terrible things
will happen if they don’t? In other words, should you entice or threaten? That’s a question Eileen Chou from the University of
Virginia and Keith Murnighan of Northwestern University set out to answer, at
least with respect to blood donation.

There are chronic shortages in the supply of blood available
for transfusions. Hopefully, the need for donated blood will someday be
eliminated by the development of artificial blood. In the meantime, however,
the Red Cross is working on getting more people to donate blood. To that end,
they took a close look at the messaging used to encourage people to donate blood.

The authors sent 3500 undergraduates one of five different emails soliciting
blood donations. One email merely stated the time
and place at which the recipient could donate blood. The other four were framed
as either saving lives (gains to be made if the subject accedes to the
request) or preventing deaths (losses to be suffered if the person doesn’t
comply). In addition, each version was presented either as being urgent or
moderately important.

Here’s the urgent, loss prevention message:

Don’t delay. Help prevent
someone from dying! Each year, 4.5 million Americans would die without blood
transfusions. Every second, 2 people could die waiting for blood. Every pint
that you donate can help them avoid dying. Don’t delay! Help prevent unnecessary
deaths.

And the moderate need, gain
message:

Act now. Help save
someone’s life! Every day, many people could be saved by donated blood. Every
pint that you donate can help them stay healthy. Act now! Promote healthy
lives.

I haven’t included the other
two variations, but you get the idea. Which message would be more likely to
drive you to the donation site? It turns out that the ‘prevent a death’ message
was far more successful than the ‘save a life’ message. More than three times
as many people showed up to donate blood after receiving the ‘loss’ message
than did for the ‘gain’ message. Interestingly, the degree of need did not seem
to matter very much. Perhaps, people already have a sense of how essential it
is to donate blood.

This greater desire to prevent
loss versus to achieve gain has been documented in other arenas. The authors of
this study performed a second study in which they tested whether requests to
prevent a charity from no longer being able to provide services would elicit
more or fewer contributions than requests to increase that charity’s services.
Again, people were more charitable to prevent losses.

I guess the lesson from this
data is that if you want someone to do something, give them the doomsday
scenario and not the possible utopia their actions could create.

Friday, March 22, 2013

We have extensive correction and repair mechanisms in our
cells to keep our DNA error free. Viruses, being minimalists, tend to skip such
extraneous functions. For better or worse (and it works both ways for them),
viruses tend to accumulate mutations at a high rate. This also means that a
fair number of new viruses are altered to the point of being ‘defective’. That
is, they lack the necessary equipment to complete their life cycle (for the
sake of argument, I’ll consider viruses to be alive). Are these defects ejected from the gene pool? Not so fast, say Ruian Ke of UCLA and his colleagues.

While it is true that defective viruses are useless on their
own, if they happen to co-infect a cell with a functional virus, they can use
the working genes from the second virus to complement whatever capabilities
they lack. But that’s not the interesting bit. It turns out that for Dengue viruses, the presence of defective viruses helps the normal viruses spread more
effectively.

This was a surprise because defective viruses were thought
to hinder their normal counterparts by depleting the resources of the infected
cell. A cell infected with both defective and normal viruses should make enough
defective viruses that can’t infect other cells to cause the infection to wind
down. Instead, the defective Dengue viruses significantly increased the transmissibility of
the normal virus. In fact, Ke and his colleagues traced the start
of some Dengue epidemics to the appearance of specific defective virus strains.

So how does this work? That’s still unknown. However, one
intriguing possibility is that the defective viruses do interfere with normal
viruses and decrease the number of infectious agents just as suspected.
As a consequence, the infected individuals don’t feel as sick and
are that much more likely to interact with other people and spread the
infection. In this scenario, there are fewer functional viruses made, but the
virus wins anyway because it still gets circulated.

If these findings prove true for other viruses, they could have
broad-ranging implications for the study of infectious viruses. To be clear, defective viruses can only cause trouble if they co-infect a cell with a complementary intact virus. We don't know how often this happens. In any case, researchers and
doctors will no longer be able to dismiss defective viruses as unimportant to
epidemiology.

Thursday, March 21, 2013

Who hasn't suffered from inadequate sleep? Whether because of overscheduling or insomnia, we all face a bleary-eyed day from time to time.

Insufficient sleep has a number
of drawbacks, including irritability and inability to think or function.
Interestingly, people who don’t get enough sleep often also succumb to weight
gain. University of Colorado researchers led by Rachel Markwald investigated
this link by limiting the sleep of some in-patient volunteers.

The scientists recruited sixteen healthy volunteers who all
ordinarily get about eight hours sleep per night. The subjects gave up coffee
and maintained a nine-hour per night sleep schedule for one week prior to the
start of the study. Over the next five days, half the participants were only
allowed to sleep five hours per night whereas the other half were given nine
hours in which to sleep. The subjects were allowed to eat as much as they
liked. After those five days, the two groups switched sleep patterns for
another five days. Thus, everyone experienced a stretch of five days getting
five hours sleep and another stretch getting nine hours sleep. Each person’s
energy expenditure was monitored 24 hours/day.

People who only slept five hours/night used about 5% more
energy than those allowed to sleep for nine hours. However, when given free
reign, they consumed about 6% more calories, resulting in a net weight gain.
After dinner snacking was the main source of additional calories during the
five-hour sleep nights. This could have been due to changes in the circadian
timing of meals, as evidenced by a delay in melatonin onset.

The order of the sleep conditions turned out to be
significant. Subjects who slept nine hours first were already eating more than
they needed (perhaps because of the novelty of being allowed unlimited food) and continued that practice after switching to five hours of sleep.
In contrast, the people who started with five hours sleep gained weight during
those five days but reduced their caloric intake after switching to nine hours
of sleep per night. In particular, women gained weight during the five-hour
regimens but lost it after switching to nine hours. Unfortunately, men overate
during both phases. This suggests that if you do have to go through an interval of shortened sleep, you should follow it up by getting plenty of sleep for a few days. This study didn't address what would happen if you underslept for a prolonged period of time. It would be interesting to know whether you'd need an equal period of regular sleep hours to reverse any weight gain.

Getting enough sleep each night is probably not all you’ll
have to do to shed a few pounds, but it might make things easier. Since
adequate sleep is important for other reasons, it’s an easy recommendation to
make.

Wednesday, March 20, 2013

I don't usually talk about holidays on this blog. My friend Cathy Earle already has them beautifully covered over at Every
Day Is Special. In this case, however, I'll make an
exception because it happens to be Brain Awareness Week. In commemoration of this
momentous week, the folks at Wellcome Trust
Centre for Neuroimaging at University College London have developed a free mobile
phone app: The Great Brain Experiment.

Screen shot of The Great Brain Experiment

As you play the games, your data
is sent back to the Wellcome Trust Centre and becomes part of a (hopefully)
huge citizen science project.

I tried the games myself and I think I did OK…once I figured out how to
play them.

Tuesday, March 19, 2013

By now, we all know that talking on the phone can diminish
our ability to drive safely. Our brains simply aren’t equipped to do more than
one thing well at a time. Researchers, led by Tom Schweizer of the University of Toronto, were interested in capturing that difference between distracted and regular driving at the level of brain activity. Traffic statistics show that distracted driving is particularly
problematic while making left turns (right turns for those of you in the United
Kingdom, Australia, or other left-driving countries). Therefore, the scientists used complex left turns for their comparison.

The researchers put sixteen volunteers in a virtual reality enhanced driving simulator
that was located within a functional magnetic
resonance imaging (fMRI) machine. The subjects were given a variety of ‘routes’
ranging from traffic-free right turns to left turns through busy intersections.
While ‘driving’, the subjects were given audio tasks designed to mimic either
conversing with passengers or talking on a hands-free phone. For example, they
were asked true or false questions, which they answered by pressing buttons on
the steering wheel.

I’m no cognitive scientist, but
even I can see that different parts of the brain are being activated during
distracted driving. The top panel shows the regions of the brain activated
during normal, non-distracted driving. It’s mostly the posterior of the brain,
containing regions critical for visual-spatial orientation that is engaged.
This is especially true while making challenging left turns (bottom row). In contrast, the
lower panel shows that when distracted, there’s a shift in activation to the
anterior of the brain where regions involved in problem solving predominate.

Brain activations from the
bottom to the top of the brain (left to right figures) of participants when
performing various simulated driving conditions.

Despite these changes in brain usage, there were no great
performance differences between distracted and undistracted driving.
Participants maintained similar speeds and lane positions during both. This is
not to say that it’s perfectly safe to talk on the phone and drive. Numerous
studies have indicated the opposite, and that even hands-free calling causes
people to be less attentive to their surroundings. This study did not evaluate
those dangers. Instead, it simply demonstrated the clear changes that occur in
brain activity between distracted and non-distracted driving. How these changes correlate with behavior requires another study.Schweizer, T., Kan, K., Hung, Y., Tam, F., Naglie, G., & Graham, S. (2013). Brain activity during driving with distraction: an immersive fMRI study Frontiers in Human Neuroscience, 7 DOI: 10.3389/fnhum.2013.00053.

Monday, March 18, 2013

Among the common symptoms of children with
autism spectrum disorder (ASD) are diminished communication and/or social
interaction. There have been many treatments proposed to alleviate this
problem, including animal therapies. Studies testing animal-assisted interactions for kids
with ASD have had generally positive results. However, those studies did not
specifically compare the benefits of animals to those of equally
engaging toys. In other words, perhaps it was the stimulation rather than anything particular about animals that helped the kids. Marguerite O’Haire of the University of Queensland and her
colleagues set the record straight: it's the animals all right.

The scientists recruited 99 children
aged 5 to 13, one third of whom were diagnosed with ASD. The kids were divided
into groups of three, with one ASD child and two neurotypical kids in each
group. After signing up, the children had an eight-week waiting period followed
by the eight-week study period during which two guinea pigs lived in their
classroom. Before and after the waiting period and after the study period, the
kids were given unstructured time to play with a variety of toys. Twice each
week during the eight-week study, the guinea pigs were brought out and handled
by the threesome.

Three of those sixteen animal
sessions (the first, last and one in the middle) were videotaped, as were the
three toy sessions. Experienced behavior coders who did not know the aims of
the study watched the tapes and evaluated the kids’ behavior. As an aside, they
used a coding system that was specifically designed for this study, the full
name of which is ‘Observation of Human Animal Interaction for Research’.
The researchers refer to it as OHAIRE, but I’m sure that’s just a coincidence.

Anyway, the children with ASD showed
more prosocial behaviors of nearly every kind (approaching others, speaking to
or looking at others, smiling) during the guinea pig sessions than they did
during the toy sessions. The only exception was that the kids with ASD spoke to
their peers more during the toy sessions (they spoke to adults more when
animals were present). Interestingly, the kids with ASD handled the toys much
more than they did the animals. Apparently, the children didn’t have to
have the guinea pigs in their laps, the animals just had to be around. This was
born out by the fact that 82% of the kids said they preferred the guinea pigs
to the toys.

No one
is suggesting that having animals around is a panacea for the problems faced by
children with ASD. However, this is one more study showing that animal therapy
does help. It’s nice that in this case, the helpers were small animals that
nearly any household or classroom could maintain. O'Haire, M., McKenzie, S., Beck, A., & Slaughter, V. (2013). Social Behaviors Increase in Children with Autism in the Presence of Animals Compared to Toys PLoS ONE, 8 (2) DOI: 10.1371/journal.pone.0057010.

Friday, March 15, 2013

Did you know there are hundreds of lakes underneath the
Antarctic ice sheet? These bodies of water, which were detected by ground penetrating radar, are about 800 meters under the ice
and are totally isolated from the outside world. This means that anything
living in those lakes has had no contact with the outside world since the lakes’
formation. This is a treat that’s too good to pass up for either biologists or astrobiologists. So far it looks
like they won’t be disappointed.Scientists have discovered that under the massive Antarctic ice sheets there lies a vast hydrological system of liquid water. This water exists because geothermal heat flow from below, coupled with pressure, movement, and the insulating nature of the ice sheet above, is great enough to maintain some areas at the base of the ice sheet above the freezing point, even in the extreme cold of Antarctica. In topographic depressions there are hundreds of lakes, both large and small; some are isolated, but many are interconnected by water channels and large areas of saturated sediments, the water eventually running out into the Southern Ocean as the ice sheet becomes a floating ice shelf.WISSARD Project.

Of course, we first have to find out what’s down there. To
that end, NASA is funding the Whillans Ice Stream Subglacial Access Research
Drilling (WISSARD) project. The goal of this project is to drill a hole
through the ice and see what’s in the lake beneath it. This is vastly more
complicated than it sounds for several reasons. To begin with, the team had to
drill a hole all the way to Lake Whillans, half a mile down through the ice. Next,
the instruments had to be threaded down that long hole and then brought back up
with samples and without scraping along the sides and becoming damaged. Also,
the instruments had to be completely sterile so as not to contaminate any
findings. And lastly, did I mention this was Antarctica? This is not the most
hospitable place in which to stand around doing fieldwork.

Alberto Behar, co-investigator of the WISSARD project, gives us a tour:

Although the findings are preliminary, there do appear to be
microbes in the subglacial lake water. This is good news for people hoping to
find life under the ice sheets of other worlds, such as Europa or Enceladus.
The next step is to see how closely these samples resemble other forms of life
on Earth.

Thursday, March 14, 2013

You may remember Joshua Pearce of
Michigan Technological University from a story I wrote five months ago. He’s
the scientist who is encouraging everyone to make their own lab equipment using
3D printers. He and his colleagues, Christian Baechler and Matthew DeVuono of
Queen's University, Ontario, have now done themselves one better. They’ve found
a way to make plastic filament (the ‘ink’ with which the printers make things)
out of discarded milk jugs.

If you have your own 3D printer, you know that you can make
an endless supply of cool and useful items. However, like Pearce, you will
undoubtedly have realized that the limiting step is keeping your printer
supplied with plastic filament. Thanks to the researchers proof of concept
designs, which they are providing for free, you too can make your own filament.

The researchers chose discarded items made of high-density polyethylene (HDPE), not because it makes the best filament (it doesn’t), but
because such items are prevalent in household waste. A variety of plastic items
including bottles made for milk, detergent and shampoo are made of HDPE. These plastic items are washed, stripped of labels, cut into pieces and fed through
an office shredder. The shreds are melted and then passed through a homemade
extruder to make the filament, which was successfully used in 3D printers.

The process does take some time. To make about 18 meters of
filament (about enough for five coffee mugs), you’d need to process 100 grams
of plastic. Just extruding that amount of melted plastic took over three hours,
and that was after washing and shredding it. Needless to say, some work needs
to be done to make the system more practical. Also, there were some consistency
issues in the diameter of the resulting filament that need to be addressed. Plus, there's the fact that HDPE isn't usually used in 3D printing. The inks of choice are PLA (Polylactic Acid) and ABS (Acrylonitrile Butadiene Styrene).

But make no mistake, Pearce and his
colleagues foresee widespread usage of this new technology. For one thing, the
process is far cheaper. You could recycle your own HDPE trash into 3D printer
filament for about a dollar a kilogram. Compare that to the current price of
commercially available filament of around $40/kg. From start to finish, the
recycling process also uses about half the energy that goes into making virgin
filament. And of course, these numbers will get much better as the process goes
large-scale and becomes automated. Finally, we’d be doing something useful with
all that HDPE trash. Saving energy and money and shrinking our landfills: a win
for everyone.

By the way, Pearce isn’t the only one
with this idea. The makers of Filabot have a shredder/extruder ready for
purchase if you’re so inclined.

Stochastic Scientist? What's up with that?

Why the Stochastic Scientist? As I'm sure you all know, 'stochastic' is another word for 'random', which is what I intend for the focus of this blog. Although my formal training is as a molecular biologist, there are many other fields of science that are also fascinating and beautiful. It's my intention to blog about which ever scientific discovery or invention catches my, and hopefully your, fancy.

I also hope to inspire people to learn more about science. By choosing among a huge variety of scientific endeavors, I'll undoubtably hit upon something that will pique my readers' interest.

I guess I could have called my blog 'The Joy of Science', but that wouldn't have been quite so random.